I moved 5 years ago and had a lot of fish, around 40 in 3 ponds. I split them into two swimming pools while we figured out their long term home and one swimming pool had 50% of the fish do exactly what you stated and fish started dying within a week, we quickly gave the rest of that pond away to someone who had space for them (and knew what happened) and the rest recovered for them. The other pool only had 1 list and eventually recover only to die a full year later (29 inches long). We ended up keeping around 10 or so fish but 3 more of them died before the new pond was built.
As others have stated moves are stressful and IMO full water changes are doing more than just changing PH and water temp. So while you are testing for PH, temp and the standard items, the overall picture is too much change in to little time is just bad for koi, tests are not good enough, IMO. Anytime you have a large change, you might get lucky and you might not, but expect bad things and hope for the best. You mentioned that both the PH and temp had changes that you then corrected, maybe a double whammy on them. When I stress them out in one direction, I don't always try and fix it right away, kind of like over correcting a steering issue.
As for you pond size, I don't follow the minimum 1,000 gallon rule, I have had under 1,000 gallon ponds work well for very long periods of time (over 20 years) with koi so as long as you are paying attention to your fish and water and working harder than those with a larger pond, you should be able to enjoy fish in your pond to as little as 300-500 gallons. The key for me with a smaller pond was to feed them slightly less so that they don't grow as fast and pollute as much and then I had larger ponds to move any fish over 12 inches.
IMO, a 500 to 1,000 gallon pond is great for sub 12 inch koi, maybe even up to 15/16, but once they hit that size consider exchanging them for some smaller koi to keep the process going. You could maybe wait to 20 inches depending on your pond, but eventually they will just need more space.
Sorry about your fish and hope you recover and get your pond back into good shape. Like you I would have also added fish back soon, I am just far to impatient.